BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 031617
(156 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LBX|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P
Length = 121
Score = 132 bits (332), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 61/120 (50%), Positives = 92/120 (76%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
KKL+K+ LK V++A++ K +KRGVKEVVK++R+G KGL VIAG+ISP DVI+H+P+LCE+
Sbjct: 2 KKLNKKVLKTVKKASKAKNVKRGVKEVVKALRKGEKGLVVIAGDISPADVISHIPVLCED 61
Query: 92 SDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDVKEL 151
+PYI++ SK+DL AGATKRPT V ++ K + G+ ++++ K + VV++V+ L
Sbjct: 62 HSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSNKKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 130 bits (327), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 60/120 (50%), Positives = 91/120 (75%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
KKL+K+ LK V++A++ K +KRGVKEVVK++R+G KGL VIAG+I P DVI+H+P+LCE+
Sbjct: 2 KKLNKKVLKTVKKASKAKNVKRGVKEVVKALRKGEKGLVVIAGDIWPADVISHIPVLCED 61
Query: 92 SDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDVKEL 151
+PYI++ SK+DL AGATKRPT V ++ K + G+ ++++ K + VV++V+ L
Sbjct: 62 HSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSNKKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|1E7K|A Chain A, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
pdb|1E7K|B Chain B, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
Length = 128
Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 35/92 (38%), Positives = 58/92 (63%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A PLA L+K+ L LV+++ +K L++G E K++ RG V+A + P+++I
Sbjct: 8 PKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIIL 67
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRPT 115
H+P+LCE+ ++PY++V SK+ L A RP
Sbjct: 68 HLPLLCEDKNVPYVFVRSKQALGRACGVSRPV 99
>pdb|2OZB|A Chain A, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|2OZB|D Chain D, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|3SIU|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIU|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIV|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|G Chain G, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|J Chain J, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
Length = 130
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 58/91 (63%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A PLA L+K+ L LV+++ +K L++G E K++ RG V+A + P+++I
Sbjct: 10 PKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIIL 69
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRP 114
H+P+LCE+ ++PY++V SK+ L A RP
Sbjct: 70 HLPLLCEDKNVPYVFVRSKQALGRACGVSRP 100
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 80.9 bits (198), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 58/91 (63%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A PLA L+K+ L LV+++ +K L++G E K++ RG V+A + P+++I
Sbjct: 24 PKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIIL 83
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRP 114
H+P+LCE+ ++PY++V SK+ L A RP
Sbjct: 84 HLPLLCEDKNVPYVFVRSKQALGRACGVSRP 114
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 77.4 bits (189), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 39/123 (31%), Positives = 67/123 (54%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A PLA L+++ L +V++AA + LK+G E K++ RG ++A + PI+++
Sbjct: 6 PKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIEILL 65
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTL 143
H+P+LCE+ ++PY++V S+ L A RP + T Q K K + L
Sbjct: 66 HLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQIYAVKDKIETLL 125
Query: 144 VVE 146
++E
Sbjct: 126 ILE 128
>pdb|1ZWZ|A Chain A, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
pdb|1ZWZ|B Chain B, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
Length = 126
Score = 77.0 bits (188), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 59/100 (59%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A PLA L+++ L +V++AA + LK+G E K++ RG ++A + PI+++
Sbjct: 6 PKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIEILL 65
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 123
H+P+LCE+ ++PY++V S+ L A RP + T
Sbjct: 66 HLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTN 105
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 76.6 bits (187), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 36/90 (40%), Positives = 54/90 (60%)
Query: 40 KLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYV 99
+L+ A+ + +K+G EV K++ RG L +IA ++ P +V+ H+P LCEE IPY YV
Sbjct: 16 ELLDAVAKAQQIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYV 75
Query: 100 ASKEDLANAGATKRPTCCVLVLTKPTKGEL 129
ASK+DL A RP V ++ + EL
Sbjct: 76 ASKQDLGKAAGVSRPASSVAIINEGDAEEL 105
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 76.3 bits (186), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 63/111 (56%)
Query: 13 KDEKKKIVSLAPIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVI 72
++E + P A PLA L+ + + LV++A +K L++G E K++ RG + ++
Sbjct: 4 QNEASEDTGFNPKAFPLASPDLNNKIINLVQQACNYKQLRKGANEATKALNRGIAEIVLL 63
Query: 73 AGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 123
A + P++++ H+P++CE+ + PY++V SK L A RP + +K
Sbjct: 64 AADAEPLEILLHLPLVCEDKNTPYVFVRSKVALGRACGVSRPVIAAAITSK 114
>pdb|3ID5|C Chain C, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3ID5|G Chain G, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3PLA|C Chain C, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|D Chain D, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|L Chain L, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
Length = 130
Score = 72.8 bits (177), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 54/88 (61%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
L+ + L+ VR+A E +K+G E K++ RG L +IA ++ P +++ H+P+LC+E
Sbjct: 18 LADKVLEAVRKAKESGKIKKGTNETTKAVERGQAKLVIIAEDVQPEEIVAHLPLLCDEKK 77
Query: 94 IPYIYVASKEDLANAGATKRPTCCVLVL 121
IPY+YV+SK+ L A + T +L
Sbjct: 78 IPYVYVSSKKALGEACGLQVATASAAIL 105
>pdb|1SDS|A Chain A, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|B Chain B, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|C Chain C, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
Length = 117
Score = 69.7 bits (169), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 53/90 (58%)
Query: 40 KLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYV 99
+L+ A+ + +K+G EV K++ RG L +IA ++ P +V+ H+P LCEE IPY YV
Sbjct: 16 ELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYV 75
Query: 100 ASKEDLANAGATKRPTCCVLVLTKPTKGEL 129
ASK+DL A + V ++ + EL
Sbjct: 76 ASKQDLGKAAGLEVAASSVAIINEGDAEEL 105
>pdb|1RA4|A Chain A, Crystal Structure Of The Methanococcus Jannaschii L7ae
Protein
pdb|1XBI|A Chain A, High Resolution Structure Of Methanocaldococcus Jannaschii
L7ae
Length = 120
Score = 69.7 bits (169), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 53/90 (58%)
Query: 40 KLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYV 99
+L+ A+ + +K+G EV K++ RG L +IA ++ P +V+ H+P LCEE IPY YV
Sbjct: 19 ELLDAVAKAQKIKKGANEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYV 78
Query: 100 ASKEDLANAGATKRPTCCVLVLTKPTKGEL 129
ASK+DL A + V ++ + EL
Sbjct: 79 ASKQDLGKAAGLEVAASSVAIINEGDAEEL 108
>pdb|1RLG|A Chain A, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
pdb|1RLG|B Chain B, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
Length = 119
Score = 69.7 bits (169), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 55/99 (55%), Gaps = 3/99 (3%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
+ L L+ + E +K+G E K++ RG L IA ++ P +++ H+P+LCEE +
Sbjct: 11 MQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKN 70
Query: 94 IPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQE 132
+PYIYV SK DL A + P ++ +GEL +E
Sbjct: 71 VPYIYVKSKNDLGRAVGIEVPCASAAII---NEGELRKE 106
>pdb|2FC3|A Chain A, Crystal Structure Of The Extremely Thermostable Aeropyrum
Pernix L7ae Multifunctional Protein
Length = 124
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 53/88 (60%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
L+++ + V+RA E +K+G E K++ RG L VIA ++ P +++ H+P+LC+E
Sbjct: 12 LAEKAYEAVKRARETGRIKKGTNETTKAVERGLAKLVVIAEDVDPPEIVMHLPLLCDEKK 71
Query: 94 IPYIYVASKEDLANAGATKRPTCCVLVL 121
IPY+YV SK+ L A + V ++
Sbjct: 72 IPYVYVPSKKRLGEAAGIEVAAASVAII 99
>pdb|2HVY|D Chain D, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|D Chain D, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|D Chain D, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 130
Score = 67.0 bits (162), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 50/74 (67%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 14 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 73
Query: 92 SDIPYIYVASKEDL 105
+IPYIYV SK++L
Sbjct: 74 KEIPYIYVPSKKEL 87
>pdb|1PXW|A Chain A, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
pdb|1PXW|B Chain B, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
Length = 128
Score = 67.0 bits (162), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 50/75 (66%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 18 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 77
Query: 92 SDIPYIYVASKEDLA 106
+IPYIYV SK++L
Sbjct: 78 KEIPYIYVPSKKELG 92
>pdb|3LWO|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
pdb|3J20|3 Chain 3, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|4 Chain 4, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 123
Score = 67.0 bits (162), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 50/74 (67%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 13 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 72
Query: 92 SDIPYIYVASKEDL 105
+IPYIYV SK++L
Sbjct: 73 KEIPYIYVPSKKEL 86
>pdb|3NMU|C Chain C, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|G Chain G, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVI|B Chain B, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVI|D Chain D, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVK|E Chain E, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|H Chain H, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 129
Score = 67.0 bits (162), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 50/74 (67%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 19 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 78
Query: 92 SDIPYIYVASKEDL 105
+IPYIYV SK++L
Sbjct: 79 KEIPYIYVPSKKEL 92
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 120
Score = 67.0 bits (162), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 50/75 (66%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 11 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 70
Query: 92 SDIPYIYVASKEDLA 106
+IPYIYV SK++L
Sbjct: 71 KEIPYIYVPSKKELG 85
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p Of
P.Horikoshii Ribonuclease P
Length = 124
Score = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 50/74 (67%)
Query: 32 KKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEE 91
K+L+++ L+ V A + +++G E K++ RG L +IA ++ P +++ H+P LCEE
Sbjct: 14 KELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEE 73
Query: 92 SDIPYIYVASKEDL 105
+IPYIYV SK++L
Sbjct: 74 KEIPYIYVPSKKEL 87
>pdb|3O85|A Chain A, Giardia Lamblia 15.5kd Rna Binding Protein
pdb|3O85|B Chain B, Giardia Lamblia 15.5kd Rna Binding Protein
Length = 122
Score = 65.9 bits (159), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 34/92 (36%), Positives = 53/92 (57%)
Query: 24 PIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVIT 83
P A P A ++LS L LV+ A + +KRG E +K + RG L +IA + PI+++
Sbjct: 5 PRAIPFANEELSLELLNLVKHGASLQAIKRGANEALKQVNRGKAELVIIAADADPIEIVL 64
Query: 84 HVPILCEESDIPYIYVASKEDLANAGATKRPT 115
H+P+ CE+ +PY+++ SK L A PT
Sbjct: 65 HLPLACEDKGVPYVFIGSKNALGRACNVSVPT 96
>pdb|1S72|F Chain F, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|F Chain F, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|F Chain F, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|F Chain F, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|F Chain F, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|F Chain F, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|F Chain F, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|F Chain F, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|F Chain F, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|F Chain F, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|F Chain F, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|F Chain F, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|F Chain F, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|F Chain F, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|F Chain F, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|F Chain F, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|F Chain F, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|F Chain F, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|F Chain F, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|F Chain F, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|F Chain F, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|F Chain F, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|F Chain F, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|F Chain F, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|F Chain F, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|F Chain F, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|F Chain F, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|F Chain F, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|F Chain F, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|F Chain F, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|F Chain F, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|F Chain F, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|F Chain F, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 120
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
L L+ + A + +K+G E KSI RG L +A ++ P +++ H+P L +E
Sbjct: 13 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 72
Query: 94 IPYIYVASKEDLANAGATKRPTCCVLV 120
+P+I+V ++DL +A + + V
Sbjct: 73 VPFIFVEQQDDLGHAAGLEVGSAAAAV 99
>pdb|3G4S|F Chain F, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|F Chain F, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|F Chain F, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
Length = 119
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
L L+ + A + +K+G E KSI RG L +A ++ P +++ H+P L +E
Sbjct: 12 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 71
Query: 94 IPYIYVASKEDLANAGATKRPTCCVLV 120
+P+I+V ++DL +A + + V
Sbjct: 72 VPFIFVEQQDDLGHAAGLEVGSAAAAV 98
>pdb|1FFK|E Chain E, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|F Chain F, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|F Chain F, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|H Chain H, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|H Chain H, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|H Chain H, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|H Chain H, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|H Chain H, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|H Chain H, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|H Chain H, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|H Chain H, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|H Chain H, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|H Chain H, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|H Chain H, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|H Chain H, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|H Chain H, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|F Chain F, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|F Chain F, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|F Chain F, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|F Chain F, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|F Chain F, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 119
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%)
Query: 34 LSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESD 93
L L+ + A + +K+G E KSI RG L +A ++ P +++ H+P L +E
Sbjct: 12 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 71
Query: 94 IPYIYVASKEDLANAGA 110
+P+I+V ++DL +A
Sbjct: 72 VPFIFVEQQDDLGHAAG 88
>pdb|3ZF7|XX Chain x, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 276
Score = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
C+ G++EV ++I + L +IA N+ PI+++ +P LC + IPY V K L +A
Sbjct: 144 CVVSGLQEVTRTIEKKTARLVLIANNVDPIELVLWMPTLCRANKIPYAIVKDKARLGDAI 203
Query: 110 ATKRPTCCVLVLTKPTKGELGQEEQDKLK 138
K TC ++ E+Q LK
Sbjct: 204 GRKTATCVAFT-------DVNAEDQAALK 225
>pdb|4A17|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 255
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 41/93 (44%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
LK G+ + I L VIA ++ PI+++ +P LC ++D+P+ +V K L
Sbjct: 124 VLKYGLNHITTLIENKQAKLVVIAHDVDPIELVIFLPQLCRKNDVPFAFVKGKAALGKLV 183
Query: 110 ATKRPTCCVLVLTKPTKGELGQEEQDKLKADYT 142
K T L + Q+ + K +Y
Sbjct: 184 NKKTATAVALTEVRNEDKAKLQQFSELFKTNYN 216
>pdb|3IZR|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 258
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
+K G+ V I + L VIA ++ PI+++ +P LC + ++PY V K L +
Sbjct: 127 VVKYGLNHVTYLIEQSKAQLVVIAHDVDPIELVVWLPALCRKMEVPYCIVKGKARLGSIV 186
Query: 110 ATKRPTCCVLVLT 122
K T VL LT
Sbjct: 187 HKK--TASVLCLT 197
>pdb|2ZKR|FF Chain f, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 266
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
L+ GV V + L VIA ++ PI+++ +P LC + +PY + K L +
Sbjct: 135 VLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGH-- 192
Query: 110 ATKRPTCCVLVLTK 123
R TC + T+
Sbjct: 193 LVHRKTCTTVAFTQ 206
>pdb|3IZS|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|G Chain G, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 256
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
+K G+ VV I L +IA ++ PI+++ +P LC++ +PY V K L
Sbjct: 131 AVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT-- 188
Query: 110 ATKRPTCCVLVLT 122
+ T V LT
Sbjct: 189 LVNQKTSAVAALT 201
>pdb|1S1I|G Chain G, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 119
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
+K G+ VV I L +IA ++ PI+++ +P LC++ +PY V K L
Sbjct: 30 AVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT-- 87
Query: 110 ATKRPTCCVLVLT 122
+ T V LT
Sbjct: 88 LVNQKTSAVAALT 100
>pdb|3JYW|G Chain G, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 113
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 50 CLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 109
+K G+ VV I L +IA ++ PI+++ +P LC++ +PY V K L
Sbjct: 25 AVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT-- 82
Query: 110 ATKRPTCCVLVLTK 123
+ T V LT+
Sbjct: 83 LVNQKTSAVAALTE 96
>pdb|3U5C|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 143
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 39 LKLVRRAA-EHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCE--ESDIP 95
LK+V R A H L RG++E K++ RG L V+ +++ ++I V L E+ +P
Sbjct: 28 LKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLANDPENKVP 87
Query: 96 YIYVASKEDLA 106
I VA + L
Sbjct: 88 LIKVADAKQLG 98
>pdb|2GN4|A Chain A, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadph And Udp-Glcnac
pdb|2GN4|B Chain B, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadph And Udp-Glcnac
pdb|2GN6|A Chain A, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp-Glcnac
pdb|2GN6|B Chain B, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp-Glcnac
pdb|2GN8|A Chain A, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp
pdb|2GN8|B Chain B, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp
pdb|2GN9|A Chain A, Crystal Structure Of Udp-glcnac Inverting 4,6-dehydratase
In Complex With Nadp And Udp-glc
pdb|2GN9|B Chain B, Crystal Structure Of Udp-glcnac Inverting 4,6-dehydratase
In Complex With Nadp And Udp-glc
pdb|2GNA|A Chain A, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp-Gal
pdb|2GNA|B Chain B, Crystal Structure Of Udp-Glcnac Inverting 4,6-Dehydratase
In Complex With Nadp And Udp-Gal
Length = 344
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 21 SLAPIAKPLAGKKLSKRTLKLVRRAAEHKCLKRGVKEVVKSIRRGHKG 68
S+ P K L K S+ + +R L GV V+KS++R H G
Sbjct: 191 SVVPFFKKLVQNKASEIPITDIRMTRFWITLDEGVSFVLKSLKRMHGG 238
>pdb|3TML|A Chain A, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|B Chain B, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|C Chain C, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|D Chain D, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
Length = 288
Score = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 68 GLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK 112
G CV+ ID + +CE+ ++P+IY S D AN + K
Sbjct: 23 GTCVVESEQMTIDTAGRLKEICEKLNVPFIY-KSSYDKANRSSGK 66
>pdb|2QND|A Chain A, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
pdb|2QND|B Chain B, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
Length = 144
Score = 26.9 bits (58), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 90 EESDIPYIYVASKEDLANA 108
EE +P+++V +K+ +ANA
Sbjct: 114 EEGXVPFVFVGTKDSIANA 132
>pdb|3V7E|A Chain A, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
pdb|3V7E|B Chain B, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
Length = 82
Score = 26.6 bits (57), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 44 RAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE 103
+ ++ K + G K+ VK+++RG V+A + PI + + V L E+ I V S +
Sbjct: 5 KVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPI-LTSSVVSLAEDQGISVSMVESMK 63
Query: 104 DLANA 108
L A
Sbjct: 64 KLGKA 68
>pdb|1T0K|B Chain B, Joint X-ray And Nmr Refinement Of Yeast L30e-mrna
Complex
pdb|3IZS|FF Chain f, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|Z Chain Z, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Z Chain Z, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|CC Chain c, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 105
Score = 26.2 bits (56), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 39 LKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPI 79
L LV ++ ++ G K VKS+R+G L +IA N +P+
Sbjct: 14 LALVIKSGKYTL---GYKSTVKSLRQGKSKLIIIAAN-TPV 50
>pdb|1CK2|A Chain A, Yeast (Saccharomyces Cerevisiae) Ribosomal Protein L30
pdb|1CN7|A Chain A, Yeast Ribosomal Protein L30
pdb|1NMU|B Chain B, Mbp-L30
pdb|1NMU|D Chain D, Mbp-L30
Length = 104
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 39 LKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPI 79
L LV ++ ++ G K VKS+R+G L +IA N +P+
Sbjct: 13 LALVIKSGKYTL---GYKSTVKSLRQGKSKLIIIAAN-TPV 49
>pdb|3JYW|2 Chain 2, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 98
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 39 LKLVRRAAEHKCLKRGVKEVVKSIRRGHKGLCVIAGNISPI 79
L LV ++ ++ G K VKS+R+G L +IA N +P+
Sbjct: 7 LALVIKSGKYTL---GYKSTVKSLRQGKSKLIIIAAN-TPV 43
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,221,127
Number of Sequences: 62578
Number of extensions: 155855
Number of successful extensions: 296
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 260
Number of HSP's gapped (non-prelim): 42
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)